1st INCF Workshop on Genetic Animal Models for Brain Diseases

The INCF Secretariat organized a workshop to focus on the “role of neuroinformatics in the processes of building, evaluating, and using genetic animal models for brain diseases” in Stockholm, December 13–14, 2009. Eight scientists specialized in the fields of neuroinformatics, database, ontologies, and brain disease participated together with two representatives of the National Institutes of Health and the European Union, as well as three observers of the national INCF nodes of Norway, Poland, and the United Kingdom

Neurocognitive Informatics Manifesto.

Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given

Usability and feasibility of consumer-facing technology to reduce unsafe medication use by older adults

Background Mobile health technology can improve medication safety for older adults, for instance, by educating patients about the risks associated with anticholinergic medication use. Objective This study's objective was to test the usability and feasibility of Brain Buddy, a consumer-facing mobile health technology designed to inform and empower older adults to consider the risks and benefits of anticholinergics. Methods Twenty-three primary care patients aged ≥60 years and using anticholinergic medications participated in summative, task-based usability testing of Brain Buddy. Self-report usability was assessed by the System Usability Scale and performance-based usability data were collected for each task through observation. A subset of 17 participants contributed data on feasibility, assessed by self-reported attitudes (feeling informed) and behaviors (speaking to a physician), with confirmation following a physician visit. Results Overall usability was acceptable or better, with 100% of participants completing each Brain Buddy task and a mean System Usability Scale score of 78.8, corresponding to “Good” to “Excellent” usability. Observed usability issues included higher rates of errors, hesitations, and need for assistance on three tasks, particularly those requiring data entry. Among participants contributing to feasibility data, 100% felt better informed after using Brain Buddy and 94% planned to speak to their physician about their anticholinergic related risk. On follow-up, 82% reported having spoken to their physician, a rate independently confirmed by physicians. Conclusion Consumer-facing technology can be a low-cost, scalable intervention to improve older adults’ medication safety, by informing and empowering patients. User-centered design and evaluation with demographically heterogeneous clinical samples uncovers correctable usability issues and confirms the value of interventions targeting consumers as agents in shared decision making and behavior change

Biomedical Informatics Applications for Precision Management of Neurodegenerative Diseases

Modern medicine is in the midst of a revolution driven by “big data,” rapidly advancing computing power, and broader integration of technology into healthcare. Highly detailed and individualized profiles of both health and disease states are now possible, including biomarkers, genomic profiles, cognitive and behavioral phenotypes, high-frequency assessments, and medical imaging. Although these data are incredibly complex, they can potentially be used to understand multi-determinant causal relationships, elucidate modifiable factors, and ultimately customize treatments based on individual parameters. Especially for neurodegenerative diseases, where an effective therapeutic agent has yet to be discovered, there remains a critical need for an interdisciplinary perspective on data and information management due to the number of unanswered questions. Biomedical informatics is a multidisciplinary field that falls at the intersection of information technology, computer and data science, engineering, and healthcare that will be instrumental for uncovering novel insights into neurodegenerative disease research, including both causal relationships and therapeutic targets and maximizing the utility of both clinical and research data. The present study aims to provide a brief overview of biomedical informatics and how clinical data applications such as clinical decision support tools can be developed to derive new knowledge from the wealth of available data to advance clinical care and scientific research of neurodegenerative diseases in the era of precision medicine

Automated Measurement of Adherence to Traumatic Brain Injury (TBI) Guidelines using Neurological ICU Data

Using a combination of physiological and treatment information from neurological ICU data-sets, adherence to traumatic brain injury (TBI) guidelines on hypotension, intracranial pressure (ICP) and cerebral perfusion pressure (CPP) is calculated automatically. The ICU output is evaluated to capture pressure events and actions taken by clinical staff for patient management, and are then re-expressed as simplified process models. The official TBI guidelines from the Brain Trauma Foundation are similarly evaluated, so the two structures can be compared and a quantifiable distance between the two calculated (the measure of adherence). The methods used include: the compilation of physiological and treatment information into event logs and subsequently process models; the expression of the BTF guidelines in process models within the real-time context of the ICU; a calculation of distance between the two processes using two algorithms (“Direct” and “Weighted”) building on work conducted in th e business process domain. Results are presented across two categories each with clinical utility (minute-by-minute and single patient stays) using a real ICU data-set. Results of two sample patients using a weighted algorithm show a non-adherence level of 6.25% for 42 mins and 56.25% for 708 mins and non-adherence of 18.75% for 17 minutes and 56.25% for 483 minutes. Expressed as two combinatorial metrics (duration/non-adherence (A) and duration * non-adherence (B)), which together indicate the clinical importance of the non-adherence, one has a mean of A=4.63 and B=10014.16 and the other a mean of A=0.43 and B=500.0

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals

A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is however critical both for basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brain-wide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brain-wide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open access data repository; compatibility with existing resources, and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.Comment: 41 page

Automated Detection of Systematic Off-label Drug Use in Free Text of Electronic Medical Records.

Off-label use of a drug occurs when it is used in a manner that deviates from its FDA label. Studies estimate that 21% of prescriptions are off-label, with only 27% of those uses supported by evidence of safety and efficacy. We have developed methods to detect population level off-label usage using computationally efficient annotation of free text from clinical notes to generate features encoding empirical information about drug-disease mentions. By including additional features encoding prior knowledge about drugs, diseases, and known usage, we trained a highly accurate predictive model that was used to detect novel candidate off-label usages in a very large clinical corpus. We show that the candidate uses are plausible and can be prioritized for further analysis in terms of safety and efficacy